In a full page ad in the Sunday New York Times, the American Civil Liberties Union appealed to President Barack Obama to keep the trial of the Sept. 11 plotters, including alleged mastermind Khalid Sheikh Mohammed, in civilian courts.

In November 2009, Attorney General Eric Holder announced that the Justice Department would try KSM in New York City near the site of the World Trade Center attacks. After initially expressing support for the trial, New York City business leaders and Mayor Michael Bloombergchanged course, complaining in January about the potential cost and disruption of a trial in Manhattan. Last week, The Washington Post reported that President Obama’s advisers are close to recommending that the DOJ return KSM to a military tribunal for prosecution.

In the ad, which features an image of Obama morphing into President George W. Bush, the ACLU calls on the president to support Holder’s original plan to try KSM and other Sept. 11, 2001, conspirators in civilian courts.

The ACLU has been critical of several of Obama’s national security and terrorism policies, saying his administration is beginning to have too many similarities to the Bush administration, such as a reliance on a “state secrets” privilege to keep information on some terrorism suspects out of court.

Anthony Romero, executive director of the ACLU, recently criticized the shift to military commissions, saying if such a change is made Obama would deal “a death blow to his own Justice Department.”

Eric Holder is facing political criticism on both sides of the aisle over his handling of terrorism detainees (file photo by Ryan J. Reilly).

Attorney General Eric Holder, who marked the anniversary of his first year in office last week, is facing a mountain of Republican criticism over his handling of terrorism issues. But at the same time, liberal organizations say they are not satisfied with the Justice Department because it has continued many of the policies of the George W. Bush administration.

On the one-year date of his Feb. 3, 2009, installation as Attorney General, Holder fought back against criticism from GOP senators, penning a letter defending the DOJ’s handling of the Christmas Day airline bomber by comparing his actions to those of the Bush Justice Department.

Meanwhile, he leads a Justice Department that has overshot its original deadline to close the Guantánamo Bay terrorism detainee facility, that has decided to detain a large chunk of the prisoners held there indefinitely and is expected, in an upcoming report, to clear the former Office of Legal Counsel lawyers who authored the so-called “torture memos.”

Late last month, the American Civil Liberties Union issued a report titled “America Unrestored” that highlighted several areas in which it said the Justice Department had not made progress in the goals it set out when President Obama took office. The report said the Obama administration had acted on only a third of the specific goals the ACLU had issued last year, many of which required action from the Justice Department.

The same talking point the Obama administration has used to push back at conservative critics of its terrorism policies — that it is continuing some of the same policies that the Bush administration put in place — points to the biggest concerns liberal organizations have with some of Holder’s decisions.

Main Justice contacted representatives and people affiliated with liberal-leaning human rights and civil liberties organizations to get their take on the biggest unresolved issues during Holder’s first year in office and to highlight a few of the biggest disagreements they have with his decisions so far:

Closing ‘Gitmo,’ but ‘Enshrining’ Indefinite Detention

While the brick-and-mortar issue of closing Guantánamo has dominated the political debate over the handling of terrorism suspects, civil liberties organizations are more upset that the Obama administration has decided to continue holding suspects without charging them in court.

Shortly after the Sept. 11, 2001, attacks, Holder told CNN that the government could hold detainees indefinitely. “It seems to me you can think of these people as combatants and we are in the middle of a war,” Holder said in a CNN interview in January 2002. “And it seems to me that you could probably say, looking at precedent, that you are going to detain these people until war is over, if that is ultimately what we wanted to do.”

His view evolved by the time Obama took office. “A great nation should not detain people, military or civilian, in dark places beyond the reach of law,” Holder said of Guantánamo in 2008 while advising the Obama transition, reported The New Yorker.

In his Senate confirmation hearing last year, Holder made clear he knew of the stakes for holding people indefinitely. “How we resolve that issue,” he said, “will say more about us as a nation than almost anything.”

But once he took office, it became clear that the government decided it could not pursue cases against some of the suspects for a variety of reasons.

President Obama, in a speech at the National Archives in May, acknowledged for the first time the need for indefinite detention. While Obama said he would “work with Congress to develop an appropriate legal regime so that our efforts are consistent with our values and our Constitution,” his administration began claiming in September that Congress authorized such powers when it approved the 2001 authorization to use force against Al Qaeda and the Taliban

Holder tried to assure people he still opposed indefinite detention. During a November meeting with retired generals who advocate the closure of the prison facility in Cuba, Holder said he shared their goal — he, too, wanted to bring the number of prisoners being held indefinitely as enemy combatants down to zero.

“He didn’t initially say that their objective was to get the number to zero, and we felt strongly that the longer we keep people with no charges indefinitely confined, it is not in our interest,” retired Gen. David Maddox told Main Justice. “He came back and said very clearly and said that was their goal, too.”

Retired Gen. David M. Maddox (photo by Ryan J. Reilly).

But a government task force studying the matter of the detainees recently finished its work and concluded, according to a Justice Department official, that 47 detainees will be held as enemy combatants, seemingly contradicting Holder’s assurance. In addition, a larger group of prisoners fall into a classification that amounts to indefinite detention, in which the government has said they can be repatriated but lacks the diplomatic ability to do so, say human rights groups.

Asked whether that reflected a change of thinking, a Justice Department spokesman said he wasn’t familiar with the Attorney General’s comments to the group of retired generals, and said that the plan to detain individuals had been laid out by the president in his May speech at the National Archives.

The indefinite detention issue has been one of the biggest disappointments to human rights organizations, but the conclusion reached by the task force, created by President Obama on his second day in office, should not come as a shock, according to Brooking Institution scholar Benjamin Wittes.

“I don’t start with the point of view that this was a surprising event or that this was something that wasn’t knowable to people who looked at the problem prospectively,” Wittes told Main Justice.

But in the political back-and-forth about Guantánamo, Witte says much of the media coverage has missed the forest for the trees — focusing on the physical facility rather than the policy of indefinite detention that it served as a symbol of.

“It’s sort of the tail wagging the dog, because if you closed it, you’d just have to rebuild it somewhere else,” said Wittes. “The issue is detention, the issue is not the choice of facility at which you do the detention.”

James P. Cullen (photo by Ryan J. Reilly)

A retired military officer just said that holding suspects without trial is generally a bad idea, and could serve as a recruitment tool for terrorists. He said there were several preferable solutions to holding detainees indefinitely, including sending them through rehabilitation programs such as the program run by Saudi Arabia.

“If we continue indefinite detention and we cannot articulate to the world why we’re doing it, then we’re simply going to move Guantánamo to Illinois or someplace else, and we’ll have a new Guantánamo North, in effect,” said retired Brigadier Gen. James P. Cullen, who advocates the closure of Guantánamo Bay through the organization Human Rights First. “We really need to be able to explain in a credible way, in a way that comports with international law and with common sense, why we’re doing it and for how long.”

Asked if he believed the president had set up the expectation that he would get rid of indefinite detention during the campaign and moved away from that position due to political pressure, an ACLU lawyer said that was really beside the point.

Benjamin Wizner, counsel to the National Security Project of the American Civil Liberties Union (photo by Ryan J. Reilly).

“For me and all of us at the ACLU, the important question isn’t what was said in the campaign, it’s what was said in the Constitution,” said Benjamin Wizner, counsel to the National Security Project of the American Civil Liberties Union.

“There’s no question that the Obama administration inherited a legal and moral mess in Guantánamo,” said Wizner. But, he said, “it’s not accomplishing much to close the prison but enshrine the principle.”

Habeas Corpus Trials

Asked about Holder’s views on holding terrorism suspects without charges, a Justice Department spokesman objected to the use of the term “indefinite detention.”

The spokesman said that Guantánamo detainees who were too dangerous, or whose trial would require the government to use evidence that was too sensitive, would continue to be able to challenge their detention in court.

“The Task Force consulted closely with the Department of Justice in conducting a legal evaluation for every detainee approved for continued detention, addressing both the legal basis for holding the detainee under the AUMF [authorized use of military force] and the government’s case for defending the detention in any habeas litigation,” said the spokesperson. “We’re confident in our ability to demonstrate to the courts that these individuals are being lawfully held under the AUMF.”

But critics say that the results of those habeas corpus trials have been scattered, chiefly because Congress has never put firm rules in place to govern prolonged detention.

In July, the chairman of the Senate Judiciary Committee called for the administration to offer details about how a prolonged detention system would operate.

Sen. Patrick Leahy (photo by Ryan J. Reilly).

“I want to understand the scope of the judicial review contemplated under this proposal before determining for myself whether it meets our standards of fair treatment under law,” said Sen. Patrick Leahy (D-Vt.) “I want to ensure that a system established by this administration is grounded in constitutional protections so that it cannot be exploited by future administrations.”

“As Justice Kennedy said in a Supreme Court decision restoring the great writ of habeas corpus, the Constitution is not something an administration is able ‘to switch on and off at will.’ I believe strongly that we can ensure our safety and security, and bring terrorists to justice, in ways that are consistent with our laws and values. I am committed to working with the president to ensure we accomplish that goal,” said Leahy.

But the Justice Department and the administration have yet to develop such a system. Given the decision of the task force last month, representatives are hopeful that such a system can be developed.

“Maybe now that the Obama administration has confessed this fact, that everybody has really known for a long time, it’s not really been a secret that there was going to be a residual population, but maybe now that they’ve said it out loud, they’ll be able to have that conversation about what the rules should be,” said Wittes, one of the authors, along with Robert M. Chesney and Rabea Benhalim, of a new report (PDF) from the Brookings Institute on indefinite detention. They write that “for good or for ill, judges must write the rules governing military detention of terrorist suspects.”

“You have this remarkable delegation of rule-making power to the lower federal courts in the first instance to kind of say who we’re going to be detaining, under what circumstances and using what procedures,” Wittes told Main Justice.

The government is arguing to keep terrorism suspects imprisoned under a legal classification that liberals, including Leahy had previously called a “legal black hole.”

“The basic outlines are still very much in flux and very much in play,” said Wittes. “There’s an enormous range of disagreement among the judges as to a large number of different issues that would be the basic building blocks of any detention system.”

Torture Memos

Critics of Bush-era detention and interrogation policies say they are disturbed by media reports that the Justice Department has watered down an ethics report about the lawyers who wrote the legal memorandums justifying enhanced interrogation methods.

Newsweek reported that the long-awaited report from the Justice Department’s Office of Professional Responsibility on the authors of the so-called “torture memos” have been cleared of professional wrongdoing.

The report, currently undergoing the process of declassification, is critical of the legal reasoning used to justify waterboarding and other enhanced interrogation techniques. But unlike a previous draft of the report, the finalized version does not conclude that the lawyers violated their professional obligations as lawyers. The reviewer, career veteran David Margolis, downgraded that assessment to say they showed “poor judgment,” sources told Newsweek.

Justice Department spokeswoman Tracy Schmaler said a redacted version of the report would be released “soon.” She declined to comment on the Newsweek article. Department policy prevents spokesman from discussing reports before they are released.

Critics of the Bush administration’s policies on the handling of terrorism suspects are now speaking out. While he hasn’t seen the investigation or the conclusion, Gen. Cullen said he was “mystified because the law and the history of the law on waterboarding is fairly clear. We have condemned that practice and we have characterized it as torture.”

Former Deputy Assistant Attorney General John Yoo helped provide the legal justification for some of the Bush administration's most controversial national security policies. (photo by Ryan J. Reilly).

“The people in the Justice Department — Jay Bybee and John Yoo and a bunch of others at the Office of Legal Counsel — were willing implementers of these policies,” Cullen told Main Justice. “They knew what the law was, they had tremendous resources and research capability. We know that ignorance of the law is no excuse, but these guys knew what the law was, they chose the violate it, and they chose to put our soldiers at significant increased risk because of what they had implemented.”

Yoo and a lawyer for Bybee did not respond to requests for comment.

Mark Filip, former Deputy Attorney General in the Bush administration, also declined to comment on the report because it had not yet been officially released.

Meanwhile, Rep. Jerrold Nadler (D-N.Y.), chairman of the House Judiciary Subcommittee on the Constitution, Civil Rights, and Civil Liberties, when told about the conclusion of the report by a blogger for FireDogLake, said, “It’s very upsetting to hear that. I should hold hearings on that. I’m interested in why a career employee would think his judgment would be better or worse” than the lawyers in the OPR who administered the initial report, he said.

The Justice Department in a Monday court filing said it can’t find 10 documents that are supposed to be released as part of a Freedom of Information Act request filed by the American Civil Liberties Union, Al Kamenreported in The Washington Post.

The ACLU’s five-year FOIA battle seeks to illuminate the process that led to a policy of harsh interrogations of terrorism suspects during the Bush administration. One of the 10 missing documents is a 59-page exchange in 2002 between the Office of Legal Counsel and the Pentagon on the eve of a decision to increase the intensity of the interrogations, Kamen reported.

The Justice Department was able to find an additional 224 documents relevant to the ACLU’s 2005 request, Kamen said. They were found in three safes and in “the back of a third drawer” inside OLC’s room for highly classified documents. The documents were located by two visiting Assistant U.S. Attorneys from New York and one DOJ attorney.

Acting Assistant Attorney General for the OLC David J. Barron had to explain the loss to a federal judge in New York. He wrote: “Due to their extreme sensitivity at the time,” the relevant document set was not copied and its contents were “intermingled” with other files in the room. The documents then took the scenic tour of Washington, D.C., first going to another special room at DOJ, then to the CIA in 2007 and stopping at the Office of Professional Responsibility until March.

Kamen reported there is no word on if or when the documents might be made public.

The Nevada U.S. Attorney office has scaled back Assistant U.S. Attorney Greg Damm’s subpoena to the Las Vegas Review-Journal seeking identifying information about people who commented on a May 26 article about an ongoing tax evasion trial, including one commenter who called Damm “evil incarnate.” Click here for our earlier report on the flap.

Now, the office is only requesting information about two comments that may be considered threatening to jurors or prosecutors.

Review-Journal Editor Thomas Mitchell has indicated he will comply with the new, much narrower, request. ”I’d hate to be the guy who refused to tell the feds Timothy McVeigh was buying fertilizer,” Mitchell said in the R-J article. But the ACLU is not satisfied. The civil liberties organization has filed a motion to quash the new subpoena.

U.S. District Judge David Ezra will have to decide whether the two comments constitute a threat to the safety of jurors or prosecutors. One of the comments refers to the jurors as “12 dummies” who should be hung if they return a conviction. The other comment came from someone who wanted to wager ”quatloos” (Star Trek currency) that one of the federal prosecutors would not reach his next birthday.

Both comments have been removed from the site because they violate the paper’s policies, the R-J reported. After the newspaper publicized the subpoena, the number of comments on the story almost doubled, from 100 to around 200, the paper said.

The scaled back subpoena bore the name of Assistant U.S. Attorney Eric Johnson, not the author of the original subpoena, Damm. This isn’t the first time Damm has been the subject of public scrutinty. Last year, Damm was blasted by the 9th Circuit Court of Appeals for witholding 650 pages of evidence from the defense.

Gregory A. Brower

Judge Kim Wardlaw wrote: “This is prosecutorial misconduct in its highest form; conduct in flagrant disregard of the United States Constitution; and conduct which should be deterred by the strongest sanction available.” Wardlaw dismissed the charges and refused to allow a retrial. Nevada U.S. Attorney Greg Brower’s spokesman Natalie Collins told Law.com that ”OPR’s investigation concluded that the U.S. Attorney’s Office did not engage in any intentional misconduct.”

The senators wrote a letter to Obama last week asking the president to block the court-ordered release of several photos that document the abuse of suspected terrorists. The American Civil Liberties Union requested the release of the photos to bring transparency to the treatment of detainees during the Bush administration. Lieberman said allowing the public to see the photos would just give into “voyeurism,” and they would be a recruiting tool for terrorists.

“There is nothing to be gained from release of these pictures and a lot to be lost,” Lieberman said at a news conference today.

The American Civil Liberties Union and the Pentagon have struck a deal for the May 28 release of many Bush-era photos documenting prisoner abuse at military prisons, TIME reported today. A journalist friend of ours who knows this story well reports the photos are expected to show abuse in Afghanistan and other locations in Iraq.

The collection includes official photos and informal pictures taken by soldiers, TIME said. The pictures, which were obtained during Defense Department investigations of military prisons, will show abuse that is “far beyond the walls of Abu Ghraib,” ACLU lawyer Amrit Singh told TIME.

“We know this could make things tougher for our troops, but the court decisions really don’t leave us with any other option,” a senior Pentagon official told TIME.

Release of the photos is a big victory for the ACLU, which has long been pressing the Pentagon for them.

The 9th Circuit Court of Appeals has returned a lawsuit against a Boeing Co. subsidiary accused of helping the government fly terrorism suspects to countries where torture is practiced back to a lower court for further consideration.

The American Civil Liberties filed the 2007 lawsuit against Jeppesen Dataplan, a San Jose-based subsidiary of Boeing, on behalf of five terrorism suspects who alleged the company contracted with the U.S. government to fly them to countries where they were tortured. The Obama administration stirred controversy when it earlier defended the Bush administration’s position that pursuit of the case would reveal state secrets.